Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,890	0	C	A	55.0%	7.3 / 52.6	40	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base C (10/8);  new base A (0/22);  total (10/30)
Fisher's exact test for biased strand distribution p-value = 5.16e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.77e-03

CTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCC‑GCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCC‑TT‑CGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTC  >  NC_000913/357740‑358033                                                                                                                                                             |                                                                                                                                                cTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCC‑GCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCC‑TT‑CGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGc‑aac                                                                                                                                                 >  2:888182/1‑151 (MQ=255)   gATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCC‑GCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCC‑TT‑CGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGc‑aacaa                                                                                                                                               <  2:343341/151‑1 (MQ=255)      aaGCGTAGCGCATCAGGCAATTCCAGCCGCAGTCCTGTTTCAGCGGCTACCGTGATTCATTTCC‑GCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCC‑TT‑CGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAAc                                                                                                                                            <  2:671430/151‑1 (MQ=255)      aaGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCC‑GCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCC‑TT‑CGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAAc                                                                                                                                            <  2:900028/151‑1 (MQ=255)          gTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCC‑GCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCC‑TT‑CGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAAccgcc                                                                                                                                        >  1:1115619/1‑151 (MQ=255)                  tCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCC‑GCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCC‑TT‑CGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTtctctc                                                                                                                                >  2:22555/1‑151 (MQ=255)                       cAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCC‑GCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCC‑TT‑CGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCagt                                                                                                                            >  2:263536/1‑150 (MQ=255)                        aaTTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCC‑GCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCC‑TT‑CGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCagt                                                                                                                            >  2:989536/1‑149 (MQ=255)                         aTTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCC‑GCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCC‑TT‑CGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCagtagt                                                                                                                         >  2:136863/1‑151 (MQ=255)                            ccAGCCACGGCCCTGTGTCGGCGCCTACCGTGTTTCATTCCC‑CCCAACACCCGCG‑TTTTAACCAAGCCCATTGTGAAAAAATGCC‑TT‑CGG‑GGCGGCTTTCGCCCAGTTTTTTTCCCGCCGA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGc                                                                                                                      <  2:1115871/151‑1 (MQ=255)                                ccgccgACCTGTTTCCGCGTCTCCCGTGATTCTTCCCC‑CCCAACACCCCCGATTTTCCCCACCCCCG‑TGTCCAAAAACGCT‑TC‑CGC‑GGCGTCGGTCTCCCAGCTTTTTTTCCGCCCC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGc                                                                                                                      <  2:381892/147‑1 (MQ=255)                                ccGCACCCCTGTGTCAGCGTCTCCGGTGTTTCATTCCC‑CCAAACACCCGCTCATTTACCCACCGCCT‑TTTCAAAAAATGCT‑TT‑CGC‑GGCGGCTTCCGGCCCGTTTTTTTCCCGCCCC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCgg                                                                                                                    <  2:1133747/149‑1 (MQ=255)                                 cGCAGCCCTGTGTCAGCGGCACCGGTAATTCTTTCCC‑GCCAACACCCGCGCTTTTACCCACCGCCT‑TGTGAAAAAATGCC‑TC‑CGC‑GGCGGCTGCCGGCCAGCTTTTTTCCCGCCGC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGc                                                                                                                 <  2:867724/151‑1 (MQ=255)                                  gCAGTCCTGTTTCAGCGCCCCCGGTATTTCTTTCCC‑GCCAACAACCGCCATTTTACCCACCCCCA‑TGTCAAAAAAGGCT‑TT‑CGG‑GGCGGCTGTCTGCCATTTTTTTTCCCCCCGC‑AACAAAGCCGCCGTTCTCTCCAGTAGTGGCgg                                                                                                                    <  2:580148/147‑1 (MQ=255)                                   cAGACCTGTGTCAGCGGCTACCGTGATTCATTTCC‑GCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCC‑TT‑CGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCgggg                                                                                                                  >  1:370142/1‑148 (MQ=255)                                       cttgtgTCGGCGGCTCCCGTGATTCTTTCCC‑CCCAACACCCCCGCATTTACCCAACGCCA‑TGTGAAAAAATGCC‑TT‑CGC‑GGCGGCTGTCTGCCAGTTATTTTCCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGc                                                                                                                 <  2:304765/143‑1 (MQ=255)                                         tgtgTCGGCGGCTACCGTGATTCATTCCC‑GCCAACACCCGCGCATTTACCAACCGCCT‑TGTGAAAAAATGCT‑TT‑CGC‑GGCGGCTGTCTGCCAGTTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGaa                                                                                                          <  2:129248/150‑1 (MQ=25)                                           tgtCAGCGGCTACCGTGATTCATTTCC‑GCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCC‑TT‑CGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGCGCCaggggaa                                                                                                         >  1:895747/1‑144 (MQ=255)                                            gtCGGCGGCTCCCGTGTTTCTTTCCC‑CCAAACACCCGCGCTTTTACCCACCGCCT‑TGTGAAAAAATCCC‑TT‑CGG‑GGGGGCTGTCTGCCAGTTTTTTTCCCGCCGC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAagag                                                                                                            <  2:143965/145‑1 (MQ=255)                                                    gcccccgttttCCTTTCCGGCCAAAAACCGC‑CTTTTTCCCAACCCCA‑TTGTCAAAAACGCCTTT‑CGG‑GGCGGCTGTCTCCCGGCTTTTTTTCCGCCGA‑AAAAAAGCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTaa                                                                                                <  2:190144/141‑1 (MQ=255)                                                            ttttcctcccccccaccaGCCGCACTTTTACCCACCGCCA‑TGTG‑AAAAATGTC‑TTCCGG‑GGCGGCTGTCAGCAATTTATTTTGCCGCCGA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTc                                                                                         <  1:590019/137‑1 (MQ=255)                                                             ttCTTTCCC‑GCAACCACCCGCGCTTTTACCCACCCCCA‑TGTAAAAAAATCCT‑TC‑CGG‑GGGGGCTGTCTCCCAGTTTTTTTCCCGCCGA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCAtg                                                                                      <  2:737220/150‑1 (MQ=255)                                                                 tttCC‑GCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCC‑TT‑CGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGaaaaaaatgtttgcacc                                                                                           >  2:144618/1‑127 (MQ=25)                                                                    cc‑GCCAACACCCGCGCTTTTACCCACCGCCA‑TGTGAAAAAATCCC‑TC‑CGC‑GGCGGCTGTCGGCCAGTTATTTTCCCGCCGC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTtgtgtg                                                                               <  2:1059290/150‑1 (MQ=255)                                                                     ccacaaacaacCGCGAATTCACCCACCACCT‑TGTGAAAAAATCCC‑TC‑GGC‑TGGGGTGGTGCCCCGGATTTTTTTCCGCCAA‑ACCAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTc                                                                                         <  2:631195/135‑1 (MQ=255)                                                                             aacCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCC‑TT‑CGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGAAAAAACATTTAACCCCTCCTGTTTTGTgggga                                                                           >  2:596628/1‑143 (MQ=25)                                                                               ccGCGCTTTTACCCAACCCCA‑TGTGCAAAAATCCT‑TT‑GGC‑GGCGGCTGTCTGCCAGTTATTTTCCCGCCGA‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgctg                                                                     <  2:673213/150‑1 (MQ=255)                                                                                             aaCCCCA‑GGTGAAAAAAGCCC‑TC‑CGG‑GGCGGCTTTCTGCCAGTTTTTTTCCCCCCGA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAtg                                                         <  2:849629/148‑1 (MQ=255)                                                                                               ccccA‑TGTGAAAAAATGCT‑TC‑CGC‑GGCGGTTGTCTCCCGGTTTTTTTCCCGCCGC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGaa                                                    <  1:845712/149‑1 (MQ=255)                                                                                                 cgcaatataaaaaaaTCC‑TT‑CGGGGGCGTCTTTCTCCCGGTTTTTTTCCCCCCGA‑AAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACaa                                                           <  2:899331/135‑1 (MQ=255)                                                                                                       ggaaaaaaTTCC‑TTGCGG‑GGCGGCTGTCTCCCGTTTTTTTTCCCGCCCA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAgg                                                 <  1:169803/145‑1 (MQ=255)                                                                                                          aaaaaTCCC‑TC‑CGG‑GGGGGCTCTCTGCCATTTTTTTTCCCCCCGA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAggg                                                <  1:714827/145‑1 (MQ=255)                                                                                                           aaaaTGCT‑TC‑CGC‑GGCGGTTGTCTGCCAGTTTTTTTCCCGCCGC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTgcg                                         <  2:508814/151‑1 (MQ=255)                                                                                                                         gggggggcTGTCTGCCAGTTTTTTTCCCGCCGA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATc                                  <  2:370231/142‑1 (MQ=255)                                                                                                                           ggcggtTGTCTGCCAGTTATTTTCCCGCCGA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCa                                 <  1:243762/146‑1 (MQ=255)                                                                                                                                   tctgctttcTATTTTTCCGCCAC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAAc                       <  2:256457/140‑1 (MQ=255)                                                                                                                                    cTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGTCAGAGAAAAAAATTTTAACTCCTCCTGTTGTGTGGCAAATGGTCCTGCTGAAAAATTGGTAAGGGGAGGGGGGCGAATCAGCTcccgcaacgc                    >  1:585064/1‑142 (MQ=255)                                                                                                                                       catgttgttttcCCGCCAA‑AAAAAATCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACcg                     <  1:184651/139‑1 (MQ=255)                                                                                                                                        ccactttttttCCCCCGCAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACcgc                    <  1:227040/141‑1 (MQ=255)                                                                                                                                         agtttttttcCCCCCGA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAAt              <  1:1032711/146‑1 (MQ=255)                                                                                                                                         acttttttcgccgcggA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTaa               <  2:697988/140‑1 (MQ=255)                                                                                                                                               tttcCCCCCGA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGt         <  2:844502/150‑1 (MQ=255)                                                                                                                                                         c‑aacaaATCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTc  <  2:371435/147‑1 (MQ=255)                                                                                                                                                             |                                                                                                                                                CTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCC‑GCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCC‑TT‑CGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTC  >  NC_000913/357740‑358033

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑